scRNA Cell Type Expression Data
Timothy Stephens
12 February, 2024
Setup
Setup R env. Load packages and set default image export formats, size and resolution.
knitr::opts_chunk$set(echo = TRUE,
fig.height = 8,
fig.width = 12,
dev = c("png", "pdf"),
dpi = 1000)
library(tibble)
library(reshape2)
library(ggplot2)
library(RColorBrewer)
library(cowplot)
library(gridExtra)
library(dplyr)##
## Attaching package: 'dplyr'## The following object is masked from 'package:gridExtra':
##
## combine## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, unionlibrary(ggh4x)
library(gtools)
options(scipen = 999) #Prevent scientific notationFunction to plot barchart
load_data <- function(sp, ct){
data <- read.table(paste("scRNA.",sp,".",ct,".filtered.long.no_genes_per_designation_LvD_and_cellType.prop.colors.tsv", sep=''),
sep='\t', header=TRUE)
u <- unique(data$Conditions)
u <- u[!u %in% c("Total")]
if("1" %in% u){
u <- mixedsort(u)
u <- c("Total", u)
} else {
u <- sort(u)
u <- c("Total", u)
}
data <- data %>%
mutate(Conditions = factor(Conditions, levels=u))
u <- unique(data$BroadCellType)
u <- u[!u %in% c("Total")]
u <- sort(u)
u <- c("Total", u)
data <- data %>%
mutate(BroadCellType = factor(BroadCellType, levels=u))
return(data)
}plot_bar_FC <- function(df,
axis.text.x.size=3,
geom_text.size=0.8,
plot.title=""
){
##
## Get colors to use for facet header/strip colors
##
df.colors <- unique(df[c("BroadCellType", "BroadCellColor")])
df.colors <- with(df.colors, df.colors[order(BroadCellType, BroadCellColor),])
t <- df.colors$BroadCellColor
names(t) <- df.colors$BroadCellType
strip <- strip_themed(background_x = elem_list_rect(fill = t))
##
## Get number of columns per panel (use either number of columns in Metacell or Cell)
##
num.columns.per.panel <- merge(
df %>%
filter(Type=="Metacell") %>%
group_by(BroadCellType) %>%
summarize(distinct_points = n()),
df %>%
filter(Type=="Cell") %>%
group_by(BroadCellType) %>%
summarize(distinct_points = n()),
by = "BroadCellType", sort=FALSE
) %>%
mutate(distinct_points = if_else(distinct_points.x > distinct_points.y,
distinct_points.x,
distinct_points.y
)
)
##
## Plot
##
# Setup bar chart
p <- df %>%
arrange(-Percent) %>%
ggplot(aes(fill=Designation, x=Conditions, y=Percent)) +
geom_bar(position=position_identity(), stat="identity") +
facet_grid2(Type~BroadCellType,
independent = "x",
scales = "free_x",
strip=strip,
switch = "y"
) +
geom_text(aes(label = Count),
hjust = -0.2,
position = position_dodge(1.0),
angle = 90,
size = geom_text.size
) +
scale_fill_manual(values=c("Dark" = "#984ea3",
"Light" = "#ff7f00"
)
) +
scale_y_continuous(expand=c(0,0), limits=c(0, max(df$Percent) * 1.05)) +
ylab("Percent genes with significant FC in a given cell type (%)") +
labs(title=plot.title) +
theme_bw() +
theme(axis.text.x=element_text(
angle = 90,
vjust = 0.5,
hjust = 1,
size = axis.text.x.size
),
plot.title=element_text(
size = 16,
hjust = 0.5
)
) +
theme(panel.border=element_blank()) +
theme(panel.grid.major.x = element_blank()) +
theme(legend.position = "none") + force_panelsizes(
rows = seq(max(num.columns.per.panel$distinct_points), length(unique(data$Type))),
cols = num.columns.per.panel$distinct_points
) +
theme(strip.text.x.top = element_text(angle = 90, size = 4, face = "bold"))
## Return plot
return(p)
}Plots
sp <- "Stylophora_pistillata_GAJOv1"
data.1 <- load_data(sp, "adult_broad_cell_type_gene_FC") %>% mutate(Type="Broad")
data.2 <- load_data(sp, "adult_cell_type_gene_FC") %>% mutate(Type="Cell")
data.3 <- load_data(sp, "adult_metacell_gene_FC") %>% mutate(Type="Metacell")
data <- rbind(data.1, data.2, data.3) %>%
mutate(Type = factor(Type, levels=c("Broad","Cell", "Metacell")))
p.SP.adult <- plot_bar_FC(data, 2.5, 0.8, plot.title=gsub("_"," ", paste(sp," Adult",sep='')))
p.SP.adult
sp <- "Stylophora_pistillata_GAJOv1"
data.2 <- load_data(sp, "polyp_cell_type_gene_FC") %>% mutate(Type="Cell")
data.3 <- load_data(sp, "polyp_metacell_gene_FC") %>% mutate(Type="Metacell")
data <- rbind(data.2, data.3) %>%
mutate(Type = factor(Type, levels=c("Cell", "Metacell")))
p.SP.polyp <- plot_bar_FC(data, 5.0, 0.8, plot.title=gsub("_"," ", paste(sp," Polyp",sep='')))
p.SP.polyp
sp <- "Stylophora_pistillata_GAJOv1"
data.2 <- load_data(sp, "larva_cell_type_gene_FC") %>% mutate(Type="Cell")
data.3 <- load_data(sp, "larva_metacell_gene_FC") %>% mutate(Type="Metacell")
data <- rbind(data.2, data.3) %>%
mutate(Type = factor(Type, levels=c("Cell", "Metacell")))
p.SP.larva <- plot_bar_FC(data, 5.0, 0.8, plot.title=gsub("_"," ", paste(sp," Larva",sep='')))
p.SP.larva
sp <- "Nematostella_vectensis_RRUSv1"
data.1 <- load_data(sp, "broad_cell_type_gene_FC") %>% mutate(Type="Broad")
data.2 <- load_data(sp, "cell_type_gene_FC") %>% mutate(Type="Cell")
data.3 <- load_data(sp, "metacell_gene_FC") %>% mutate(Type="Metacell")
data <- rbind(data.1, data.2, data.3) %>%
mutate(Type = factor(Type, levels=c("Broad","Cell", "Metacell")))
p.NV <- plot_bar_FC(data, 3.0, 0.8, plot.title=gsub("_"," ", paste(sp,"",sep='')))
p.NV